Documentation Index
Fetch the complete documentation index at: /llms.txt
Use this file to discover all available pages before exploring further.
Environment variables about the analysis and sample are injected into every workflow for your convenience.
| Environment Variable | Description |
|---|---|
OCX_SAMPLE_FILENAME | The normalized filename of the FASTA/Q file that was uploaded to One Codex. This will correspond to the name of the file that is injected into the working directory for your workflow. |
OCX_SAMPLE_NAME | The name of the Sample in One Codex. This might be different from the filename if the user has edited the Sample metadata. |
OCX_SAMPLE_UUID | The UUID of the Sample in One Codex. This is a globally unique identifier for the Sample that was used as input for the workflow. |
OCX_ANALYSIS_UUID | The UUID of the current Analysis in One Codex. This is a globally unique identifier for the current workflow run on a particular sample with the specific set of input parameters. This can be used to globally identify a particular instance of an Analysis in One Codex. |
OCX_CPU_REQUEST | The number of CPUs requested for your workflow. Pass this to multi-threaded tools so they use all the CPUs available to the run. |
OCX_INSTRUMENT_VENDOR | The name of the sample’s instrument vendor (e.g., “Illumina”, “Oxford Nanopore”). |
OCX_IS_LONG_READ | "true" if the sample is detected to be from a long read sequencer (e.g., PacBio or ONT); "false" otherwise. |
OCX_DEPENDENCY_UUIDS | Space-separated list of Analysis UUIDs that the current analysis depends on. |
REPOSITORY_DIR | The name of the directory in the working directory that your workflow’s Git repository was cloned into (e.g. my-pipeline for https://github.com/my-org/my-pipeline). Only set if the workflow has a Git repository configured. See Connecting your GitHub Repository. |
